Kimihiko Kimizuka has found himself inadvertently entangled in various crimes more times than he can remember, referring to himself as a magnet for trouble. One day, as if it was nothing out of the ordinary, a group of unknown men kidnaps him, forcing him to board a flight—where he also encounters a hijacking. Amid the resulting chaos, however, Kimizuka meets a stunning silver-haired beauty, going by the codename Siesta, who then saves the day. Claiming to be a legendary detective, Siesta enlists Kimizuka to be her sidekick. Though Kimizuka refuses at first, with Siesta's insistence, he eventually joins her—marking the start of a grand adventure spanning the entire world, preventing multiple threats that could spell doom for humanity along the way. Unfortunately, after three years of their unpredictable yet enjoyable time together, Siesta abruptly passes away. Distraught, Kimizuka tries to leave all memories of her behind, but as he begins to meet more people, it seems that Siesta's influence will never truly die.

Bullies often target someone frail and weak—someone exactly like Yuugi Mutou. His beautiful childhood friend, Anzu Mazaki, is always there to stand up for him, but he can't depend on her forever. Katsuya Jonouchi, who is almost always accompanied by his verbal sparring partner Hiroto Honda, doesn't seem like a bad person either, despite always bringing Yuugi trouble. But most of all, Yuugi wishes for a true friend who understands him and would never betray him. Yuugi treasures his Millennium Puzzle, an ancient Egyptian artifact that was brought into his grandfather's game shop. Believing that solving the puzzle will grant him his wish, he completes the puzzle, unleashing a new personality within him—the soul of the King of Games. Dark, twisted, strong, and reliable, the new personality named Yami Yuugi is the exact opposite of Yuugi. Upon any injustice toward him, Yami Yuugi takes over Yuugi's body and forces the opponent into a Shadow Game. The stakes are high as whoever loses shall have a taste of the darkness that resides within their own heart.

The dispassionate, transforming assassin Golden Darkness returns to peer deeper into the mysteries surrounding her new life, while a sinister Nemesis manipulates her younger sister Mea from the shadows. Along with their newly discovered mother, Tearju, this previously estranged family quickly becomes the center of everyone's attention. On the other hand, Princess Momo's Harem Plan stands on shaky ground amidst Rito's inability to confess to his longtime crush Haruna, who has grown feelings of her own. But things aren't as peaceful as they seem; an evil force looms amidst the innocuous commotion, threatening to eclipse the love, happiness, and friendship of Rito and his harem. Only the light of love can hope to banish the shadow.

A.D. 2016, the foundations of humanity have been incinerated by the Mage King Solomon. Chaldea, a secret mages organization with the mission to preserve humanity's future, foresaw mankind's extinction in 2015. Thus commenced the operation to repair the Singularities in history caused by Holy Grails dispersed across time and space—Operation Grand Order. Using the Rayshift time travel technology, Chaldea's last master Ritsuka Fujimaru and his demi-servant Mash Kyrielight have traveled to and resolved six Singularities. Now, they depart for their most dangerous destination yet: a civilization in the Age of Gods, B.C. 2655 Mesopotamia. Ritsuka and Mash soon discover that Demonic Beasts roam the land, attacking people and towns. Amidst chaos and terror lies humanity's last defense—Uruk, a fortress city that acts as the frontline for the battle against the beasts. The battlefront is commanded by none other than King Gilgamesh, the King of Heroes, who sought aid from Heroic Spirits and took on the role of a mage to protect his city. Along with Gilgamesh and the summoned servants, Ritsuka and Mash must protect Uruk against the magical beasts' onslaught and defeat the Three Goddess Alliance who aims to eradicate humankind; all the while, a greater threat looms over Uruk, preparing for its awakening.